Contacts of the helix formed by residues 207 - 214 (chain E) in PDB entry 5EJK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197E ASN 3.7 8.5 - - - -
198E HIS 3.4 20.9 - - - +
199E PHE 4.2 2.0 - - - -
200E GLU* 3.3 28.9 - - - +
206E LYS* 1.3 76.3 - - - +
208E PRO* 1.3 68.8 - - - +
209E ILE* 3.3 7.6 - - - +
210E GLN* 2.9 41.5 + - + +
211E LYS* 2.8 30.2 + - - +
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Residues in contact with PRO 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E SER* 3.4 25.8 - - - +
86E SER* 3.6 16.2 - - - +
87E ALA* 4.1 7.4 - - - +
196E LEU 3.5 4.5 - - - +
197E ASN* 3.3 11.4 - - - +
199E PHE 3.3 19.3 - - - +
201E ARG* 3.3 42.6 - - + +
206E LYS 4.2 2.7 - - - +
207E THR* 1.3 83.5 - - - +
209E ILE* 1.3 56.2 + - - +
211E LYS* 3.7 6.3 - - - -
212E HIS* 2.9 27.5 + - - +
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Residues in contact with ILE 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E VAL* 6.5 1.1 - - + -
112E MSE 6.0 4.0 - - + -
197E ASN* 3.0 31.9 + - + +
198E HIS* 3.9 30.5 - - + +
207E THR* 3.3 11.2 - - - +
208E PRO* 1.3 73.9 - - - +
210E GLN* 1.3 66.5 - - + +
212E HIS* 4.1 8.7 - - + +
213E TRP* 2.9 59.9 + - + +
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E LYS* 4.3 22.7 + - + +
207E THR* 2.9 34.1 + - - +
209E ILE* 1.3 78.7 - - + +
211E LYS* 1.3 57.5 + - - +
212E HIS 3.1 1.3 - - - -
213E TRP* 5.4 0.4 - - - -
214E ARG* 2.7 56.7 + - + +
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Residues in contact with LYS 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E PRO* 3.6 6.2 - - - +
84E ALA 4.6 7.6 + - - +
85E SER* 3.6 16.1 - - - +
86E SER* 2.9 29.6 + - - -
201E ARG* 5.4 0.4 - - - +
204E ASN* 2.9 43.7 + - - +
205E THR* 5.9 1.8 - - + -
206E LYS* 3.7 24.9 - - + -
207E THR 2.8 15.9 + - - +
208E PRO* 3.7 17.1 - - - +
210E GLN* 1.3 73.2 - - - +
212E HIS* 1.3 59.4 + - - +
214E ARG 4.2 5.6 - - - -
215E PRO* 3.5 23.4 - - + +
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Residues in contact with HIS 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E PRO* 3.6 23.9 - - + +
58E LEU* 4.1 13.3 - - + +
82E ASP* 4.9 0.4 - - + -
85E SER* 3.4 26.9 - - - +
87E ALA* 4.9 3.8 - - + -
112E MSE 3.3 59.7 + - + +
208E PRO 2.9 18.0 + - - +
209E ILE* 3.5 13.9 - - + +
210E GLN 3.1 0.4 - - - -
211E LYS* 1.3 78.7 - - - +
213E TRP* 1.3 93.7 + + - +
215E PRO* 3.5 11.4 - - - +
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Residues in contact with TRP 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 5.7 4.3 - - + -
111E VAL 4.2 16.6 - - - -
112E MSE 4.1 16.6 - - + -
209E ILE* 2.9 57.0 + - + +
210E GLN* 5.4 0.2 - - - -
212E HIS* 1.3 93.9 + + - +
214E ARG* 1.3 68.3 + - + +
215E PRO* 3.5 5.1 - - - +
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Residues in contact with ARG 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E LYS* 5.2 5.5 - - - +
210E GLN* 2.7 44.7 + - + +
211E LYS* 4.2 1.6 - - - -
213E TRP* 1.3 83.5 - - + +
215E PRO* 1.3 65.5 - - - +
216E THR* 3.9 4.0 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il